There is an inaccurate statement in this article.
The authors did not say there is no evidence of an infectious cause in ME/CFS, only that XMRV and pMLV do not cause it.
In a Twiv podcast with Dr. Vincent Racaniello, Dr. Lipkin stated that many patients in previous studies have shown polyclonal B-cell activation and that research into the microbiome and biomarkers continues including work at the CII.
He stated that the bulk of the funds invested in the study went toward patient selection (specific case definitions (there are many), psychiatric disorders causing fatigue were excluded, patients had an infectious trigger etc,) and sample collection. This leaves sufficient samples for nearly fifty more studies is this rigorously defined population according to Lipkin.
The full podcast is available on iTunes or on Dr. Racaniello's blog.

This is definitely not the first time that human genes are found in bacteria or vice versa: Trost et al have published two papers on this showing that ALL human proteins contain bacterial consensi,often of contiguous nonapeptides, and therefore genes (and therefore that bacteria contain human genes)
Bacterial peptides are intensively present throughout the human proteome Self/Nonself
Trost et al, 2010at
and No human protein is exempt from bacterial motifs. Not even one Self Nonself Trost et al, 2010b